GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Acidovorax sp. GW101-3H11

Align Homocysteine/cysteine synthase; O-acetylserine/O-acetylhomoserine sulfhydrylase; OAS-OAH SHLase; OAS-OAH sulfhydrylase; EC 2.5.1.47; EC 2.5.1.49 (characterized)
to candidate Ac3H11_1341 O-acetylhomoserine sulfhydrylase (EC 2.5.1.49) / O-succinylhomoserine sulfhydrylase (EC 2.5.1.48)

Query= SwissProt::P06106
         (444 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_1341
          Length = 442

 Score =  392 bits (1007), Expect = e-113
 Identities = 204/435 (46%), Positives = 279/435 (64%), Gaps = 20/435 (4%)

Query: 5   FDTVQLHAGQENPGDNAHRSRAVPIYATTSYVFENSKHGSQLFGLEVPGYVYSRFQNPTS 64
           F T  +HAG +   D    +RA PI+ TTS+VF+N++H S LF L+  G VYSR  NPT 
Sbjct: 15  FGTRAIHAGAQP--DPVTGARATPIHQTTSFVFDNAEHASSLFNLQTFGNVYSRISNPTV 72

Query: 65  NVLEERIAALEGGAAALAVSSGQAAQTLAIQGLAHTGDNIVSTSYLYGGTYNQFKISFKR 124
            V EERIA+LE G AALA +SG AAQ  A+  +  TGD+IV+ S LYGGT  Q  + F R
Sbjct: 73  AVFEERIASLENGRAALACASGMAAQMAALLAILKTGDHIVAASTLYGGTVGQLGVGFAR 132

Query: 125 FGIEARFVEGDNPEEFEKVFDERTKAVYLETIGNPKYNVPDFEKIVAIAHKHGIPVVVDN 184
            GIE  FV+  +PE F +     T+AVY ETIGNP  NV D   +  +AH HG+P+++DN
Sbjct: 133 LGIETTFVDPADPENFARAMRPNTRAVYGETIGNPLVNVLDIAAVAEVAHAHGVPLIIDN 192

Query: 185 TFGAGGYFCQPIKYGADIVTHSATKWIGGHGTTIGGIIVDSGKFPWKDYPEKFPQFSQPA 244
           T  A  Y C P+  GADIV HSATK+IGGHGTT+GG++V+ G+FPW +   KFP+  +P+
Sbjct: 193 TV-ASPYLCNPLALGADIVVHSATKYIGGHGTTMGGVVVEGGQFPWDN--GKFPEMVEPS 249

Query: 245 EGYHGTIYNEAYGNLAYIVHVRTELLRDLGPLMNPFASFLLLQGVETLSLRAERHGENAL 304
             YHG  + E +G+  Y +  R E+ R  G +++P  ++ LLQG ETL LR   H  NAL
Sbjct: 250 RAYHGVKFYETFGDFGYTMKARMEVNRTFGGVLSPMNAWQLLQGAETLHLRMREHCRNAL 309

Query: 305 KLAKWLEQSPYVSWVSYPGLASHSHHENAKKYL-----SNGFGGVLSFGVKDLPNADKET 359
            +AK+L+  P V+WV+YPGL+   + + A+K       + G  G+L+FGVK    A    
Sbjct: 310 AVAKFLQSHPQVAWVNYPGLSDSPYFDLAQKQFRAVDGAPGASGILTFGVKGGATA---- 365

Query: 360 DPFKLSGAQVVDNLKLASNLANVGDAKTLVIAPYFTTHKQLNDKEKLASGVTKDLIRVSV 419
                 G + +D  +  S+LAN+GDAKTLVI P  TTH+QLN++E   +GV+ D++R+SV
Sbjct: 366 ------GEKFIDACEFLSHLANIGDAKTLVIHPASTTHRQLNEEELARAGVSADMVRLSV 419

Query: 420 GIEFIDDIIADFQQS 434
           GIE +DDI+ D  Q+
Sbjct: 420 GIEDLDDILWDIDQA 434


Lambda     K      H
   0.317    0.136    0.402 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 588
Number of extensions: 28
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 444
Length of database: 442
Length adjustment: 32
Effective length of query: 412
Effective length of database: 410
Effective search space:   168920
Effective search space used:   168920
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory